get.cross.K: Cross type K function using homotypic and heterotypic case...

In IDSpatialStats: Estimate Global Clustering in Infectious Disease

Cross type K function using homotypic and heterotypic case types

Description

A wrapper function of the Kcross function from the spatstat.explore package (Baddeley et al. 2016) that takes epidemiological data used by IDSpatialStats functions and calculates the cross type K-function based on user defined case type homology

Usage

get.cross.K(epi.data, type, hom, het = NULL, r = NULL, correction = "none")

Arguments

epi.data	a three-column numerical matrix that contains coordinates (x and y) for each case and information on case type (e.g. genotype or serotype). First two columns must be x and y
type	an integer giving the column that contains information on case type. Must be an integer or a character
hom	a scalar or vector giving the homotypic case type(s). Equivalent to the 'j' point type used in the cross K function. Must be an integer or character
het	a scalar or vector giving the heterotypic case type(s). Equivalent to the 'i' point type used in the cross K function. The default is NULL, which uses any case type not defined in the hom argument as heterotypic. Must be an integer or a character
r	a numeric vector giving the spatial distances
correction	type of edge correction to be applied (default set to 'none'). See the Kcross function in the spatstat.explore package for more details

Value

a data frame with a minimum of three columns giving the radius (r), the theoretical value of the K function for a Poisson process (theo), and value of the K function evaluated at radius r. The column name gives the type of edge correction used

Author(s)

John Giles

References

Baddeley A, Rubak E, and Turner R. (2016). "Spatial Point Patterns: Methodology and Applications with R". CRC Press.

Examples

data(DengueSimR01)

k <- get.cross.K(epi.data=DengueSimR01, type=5, hom=2, het=NULL, r=NULL, correction='border')

plot(k[,2], type='l', col='red', lty=2, xlab='r', ylab='cross K function')
lines(k$border)

IDSpatialStats documentation built on Sept. 11, 2024, 5:14 p.m.